Place some frame protectors; there's a variety of ways to do this, plenty of threads on the subject. The housings are doing the rubbing, hopefully, not the cables. Shorten the housing (and cables as necessary) where you can to eliminate extraneous rub; if you're not capable of doing this for yourself go back to the shop and explain your concerns and see what they can offer to reduce it and/or place frame protectors where needed.

I can't tell if you have them or not, but if you want to protect your frame further, you can buy these little rubber o-rings that you put on the INNER cable, where it's exposed between the cable housings. Your LBS should have them and it only requires, well, removing all the cable's again. That or you can buy a plastic sheath (think of a long skinny plastic straw) that does the same thing.

While it's not usually a problem it happens sometimes. Just keep it in mind.